Comparative mitogenomic and phylogenetic analysis of Apalone spinifera and Apalone ferox (Testudines: Trionychidae).

By using 6 years of Long Term Resource Monitoring Program (LTRMP) turtle by-catch data collected from the middle Mississippi River, we investigated smooth softshell (Apalone mutica) and spiny softshell (Apalone spinifera) turtle abundance collected from 5 physical habitats: main channel border, wing dikes, tributary, open side channel, and closed side channel. Females comprised 62% and males 38% of the total catch of smooth softshell turtles. For spiny softshell turtles, females comprised 67% and males 33% of the total catch. We observed skewed reproductive age structure and sex ratios among and within both species. Smooth and spiny softshell turtle captures were dominated by reproductive individuals (62% and 87%, respectively). Smooth softshell turtles were most abundant in open side channels and main channel borders, whereas spiny softshell turtles were most abundant in tributaries and closed side channels. Smooth softshell abundance was greatest in deep waters with faster water velocity, whereas spiny softshell abundance was greatest in waters with higher visibility (e.g., Secchi transparency) and slower water velocity.

Pelochelys cantorii has become one of the most critically endangered species in the world. The complete mitochondrial DNA (mtDNA) genome of P. cantorii (Guangning) was generated by polymerase chain reaction (PCR) amplification, primer-walking sequencing and fragment cloning. The mitochondrial genome is 17,424 base pairs (bp) and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. Comparative analyses of complete mitochondrial genome sequences from different habitats, we found that the P. cantorii (unknown) may be wrong identified. And the phylogenetic position of P. cantorii also support this result, maximum likelihood (ML) and Bayesian (BI) analyses were conducted based on 12 heavy-strand PCGs and 2 rRNAs from 18 taxa. P. cantorii (unknown) is not closely related to other P. cantorii, but formed a clade with Apalone spinifera and Apalone ferox.

Softshell turtles (Family Trionychidae) possess extensive webbing between the digits of the manus, suggesting that the forelimb may serve as an effective thrust generator during aquatic locomotion. However, the hindlimb has previously been viewed as the dominant propulsive organ in swimming freshwater turtles. To evaluate the potential role of the forelimb in thrust production during swimming in freshwater turtles, we compared the forelimb morphology and three-dimensional forelimb kinematics of a highly aquatic trionychid turtle, the spiny softshell Apalone spinifera, and a morphologically generalized emydid turtle, the red-eared slider Trachemys scripta. Spiny softshells possess nearly twice as much forelimb surface area as sliders for generating drag-based thrust. In addition, although both species use drag-based propulsion, several aspects of forelimb kinematics differ significantly between these species. During the thrust phase of the forelimb cycle, spiny softshells hold the elbow and wrist joints significantly straighter than sliders, thereby further increasing the surface area of the limb that can move water posteriorly and increasing the velocity of the distal portion of the forelimb. These aspects of swimming kinematics in softshells should increase forelimb thrust production and suggest that the forelimbs make more substantial contributions to forward thrust in softshell turtles than in sliders. Spiny softshells also restrict forelimb movements to a much narrower dorsoventral and anteroposterior range than sliders throughout the stroke, thereby helping to minimize limb movements potentially extraneous to forward thrust production. These comparisons demonstrate considerable diversity in the forelimb kinematics of turtles that swim using rowing motions of the limbs and suggest that the evolution of turtle forelimb mechanics produced a variety of contrasting solutions for aquatic specialization.

Levisunguis subaequalis Curran, Overstreet, Collins & Benz, 2014 , was recently described from the lungs of the definitive hosts, softshell turtles, Apalone ferox (Schneider, 1783), and Apalone spinifera aspera (Agassiz, 1857) as well as the viscera of an intermediate host, the western mosquitofish, Gambusia affinis (Baird and Girard, 1853). However, the original account lacked molecular data. Furthermore, histological examination of infected host tissues in the original account of L. subaequalis did not reveal any pathological changes in the intermediate host. The present work provides a robust morphological description of the nymph and novel molecular data from the 18S and 28S ribosomal gene regions and the cytochrome c oxidase subunit 1 (COI) mitochondrial gene. Phylogenetic analyses using Bayesian inference and maximum likelihood analysis with concatenated sequence data from these 3 regions, as well as each region individually, placed the turtle pentastomid L. subaequalis as a sister clade to the crocodilian pentastomids of the genus Sebekia Sambon, 1922. While only concatenated phylogenetic analyses agreed with the currently accepted classification of the Eupentastomida and phylogenetic signal assessment indicated that the concatenated data set yielded the most phylogenetic signal, data from more taxa are still needed for robust phylogenetic inferences to be made. The intensity of infection ranged from 2 to 171 nymphs per fish, compared with the highest previously reported intensity of 6. These high-intensity infections with L. subaequalis were characterized by the nymphs occupying 5-50% of the coelomic cavity of G. affinis. However, despite this heavy parasite infection, fish exhibited minimal pathology. Observed pathology was characterized by compression or effacement of organs adjacent to the nymphs, particularly liver, swim bladder, and intestines, as well as the formation of granulomas around shed pentastomid cuticles. Nonetheless, the morphological and molecular data provided in the present work will bolster future efforts to identify this pentastomid in other hosts where pathology may be present in addition to aiding in the advancement of the field of molecular pentastomid systematics.

Softshell turtles (Apalone spinifera) were submerged at 3 degrees C in anoxic or normoxic water. Periodically, blood PO(2), PCO(2), pH, plasma [Cl(-)], [Na(+)], [K(+)], total Ca, total Mg, lactate, glucose, and osmolality were measured; hematocrit and body mass determined; and blood [HCO(3)(-)] calculated. On day 14 of anoxic submergence, five of eight softshell turtles were dead, one died immediately after removal, and the remaining two showed no signs of life other than a heartbeat. After 11 days of submergence in anoxic water, blood pH fell from 7.923 to 7.281 and lactate increased to 62.1 mM. Plasma [HCO(3)(-)] was titrated from 34.57 mM to 4.53 mM. Plasma [Cl(-)] fell, but [K(+)] and total Ca and Mg increased. In normoxic submergence, turtles survived over 150 days and no lactate accumulated. A respiratory alkalosis developed (pH-8.195, PCO(2)-5.49 after 10 days) early and persisted throughout; no other variables changed in normoxic submergence. Softshell turtles are very capable of extrapulmonary extraction of O(2), but are an anoxia-intolerant species of turtle forcing them to utilize hibernacula that are unlikely to become hypoxic or anoxic (e.g., large lakes and rivers).

Previous data of the whole mitochondrial genome of soft-shelled turtle that it’s available in a public repository: Dogania subplana, Pelochelys cantorii, Chitra indica, Trionyx triunguis, Apalone spinifera, Rafetus swinhoei, and Pelodiscus sinensis. The first two species have natural distribution in Indonesia. Amyda cartilaginea is a species of soft-shelled turtle that is abundant in Indonesia. However, the whole mitochondrial genome data of A. cartilaginea is not available. This study aims to characterize the partial mitochondrial genome and analyze the phylogenetic position of A. cartilaginea. We reported almost complete mitochondrial genome of A. cartilaginea that caught from Batanghari river in Dharmasraya District, West Sumatera. The amplification of mitochondrial DNA fragments was performed using several primers designed following mitochondrial gene organization and sequence of D. subplana (Accession No AF366350). We sequenced half of the whole mitochondrial genome (7757 bp, 48%). The gene organization of the mitochondrial genome of A. cartilaginea was identic with D. subplana and P. cantorii. The phylogenetic tree analysis based on 16SrRNA revealed that the position of A. cartilaginea clustered with another soft-shelled turtle. Further study is needed to make a complete sequence of the mitochondrial genome of A. cartilaginea, with special focus on the control region to be applied to sustainable wild population management.

Turtles face unique conservation challenges in modern modified river systems. Despite their ecological importance, gaps in knowledge still exist that may hinder their conservation. Turtle by-catch data from the US Army Corps of Engineers' Long-Term Resource Monitoring Program were analyzed for 5 turtle species (false map turtle, Graptemys pseudogeographica; red-eared slider, Trachemys scripta; common snapping turtle, Chelydra serpentina; smooth softshell turtle, Apalone mutica; and spiny softshell turtle, Apalone spinifera) to better understand macrohabitat and mesohabitat use. These species demonstrated differences in habitat use between various macrohabitats, substrata, velocity classes, and depth classes. Common snapping turtles and spiny softshell turtles were captured most often in tributaries, whereas red-eared sliders were captured most often in tributaries and closed side channels. Smooth softshell turtles used open side channels and unstructured main-channel borders most often. False map...

Softshell turtles (Trionychidae) display characteristic pits and ridges, or "sculpturing," on the bony carapace. Variation in sculpturing pattern may be useful in classifying fossilized shell fragments. Although past attempts could discern qualitative differences in certain best-case scenarios, many early taxonomic uses of sculpturing traits have been reevaluated as unreliable in the face of intraspecific variation. The potential of sculpturing to contain consistently reliable, quantitative, taxonomically informative traits remains underexplored. Here, we revisit this idea by quantifying trionychid shell patterning with topographic measurement techniques more commonly applied to nonhomologous quantification of mammalian teeth and geographic surface topography. We assess potential sources of variation and accuracy of these metrics for species identification. Carapaces of extant specimens used in this study included members of the species Apalone ferox, Apalone spinifera, and Amyda cartilaginea and were obtained from the herpetology collections of the Florida Museum of Natural History. 3D scans of shells were systematically sampled to create digital "fragments." These fragments were quantified using three topographic measurements: Dirichlet Normal Energy (DNE), Relief Index (RFI), and Orientation Patch Count Rotated (OPCR). A nested MANOVA suggests there is significant variation at the species, individual, and carapace location levels of analysis. Linear discriminant analysis correctly predicts a sample's species identity from DNE, RFI, and OPCR 75.2% of the time. These promising results indicate that topographic measures may provide a method for identifying shell fragments that are currently identifiable only as Trionychidae indet. Future work should explore this approach in additional species and account for ontogenetic changes.

The red-eared slider, Trachemys scripta elegans (Wied, 1938), has been introduced worldwide, partly because of the exotic pet trade in the 1980s and 1990s. When T. s. elegans is released or escapes into natural environments, it often establishes new feral populations due to its tolerance for a variety of aquatic ecosystems. Therefore, it is now considered one of the most invasive species in the world because it can compete with native turtle species. In the present study, our objectives were to identify the potential for polystome spillover and spillback resulting from the introduction of the red-eared slider into new environments in North America. Fieldwork investigations were thus conducted mainly in aquatic habitats in Florida and North Carolina, United States, but also in Connecticut, Indiana, Kansas, Maine, Nebraska and New York. Using DNA barcoding based on cytochrome c oxidase I (COI) sequences, we surveyed the species diversity of polystome within American freshwater turtles. These included T. s. elegans but also Apalone ferox, Apalone spinifera, Chelydra serpentina, Chrysemys picta, Kinosternon baurii, Pseudemys spp., Sternotherus minor and Sternotherus odoratus. Genetic evidence confirmed that invasive populations of T. s. elegans in southern Europe have transmitted their own polystomes to native host species following spillover effects, and revealed here that T. s. elegans in non-indigenous habitats in the United States acts as a new reservoir of infection for native polystomes following spillback effects, thus increasing indigenous parasite transmission in the wild. Together, these findings raise further concern about the spread of non-native turtles and their impact on parasite transmission.

Effect of acclimation temperature and substrate type on selected temperature, movement and activity of juvenile spiny softshell turtles (Apalone spinifera) in an aquatic thermal gradient.

The nuclear–follower relationship is a specialized interspecific foraging association in which the nuclear species excavates the substrate while foraging, and follower species access food items flushed or uncovered by the nuclear species. We observed a nuclear–follower association between Apalone spinifera (Spiny Softshell Turtle) and fish (Micropterus salmoides [Largemouth Bass] and Lepomis spp.) in an urban drainage canal (Wards Creek) in Baton Rouge, LA, during June and July of 2020. Groups of Largemouth Bass and Lepomis spp. numbering 0–2 and 1–20, respectively, followed foraging Spiny Softshell Turtles. When foraging, Spiny Softshell Turtles were observed moving along the creek bottom, thrusting their probosces into and vigorously excavating the substrate. The accompanying fish then entered the cloud of suspended sediment to pursue and capture prey. Excavation of the substrate by Spiny Softshell Turtles appears to be the critical component of this nuclear–follower relationship, flushing or exposing prey that would otherwise be unavailable to fish. This nuclear–follower relationship is apparently one of commensalism, i.e., while fish probably benefit from increased foraging success, few if any benefits accrue to foraging turtles.

Fish mitochondrial genome have been largely studied worldwide for evolutionary and other genetic purposes and the structure and gene organization are commonly conservative. However, several studies have demonstrated that this scenario may present variations in some taxa, showing differentiation on the gene rearrangement. In this study, the complete mitogenome of terrestrial fish Boleophthalmus dussumieri was generated and compared with other species of the Exudercidae fishes. The newly complete mitogenome generated is circular and 16,685 bp of length, and it contained 13 protein-coding genes (PCGs), two ribosomal RNA (rRNAs), 22 transfer RNA genes (tRNAs), and one control region (CR), with high conservative structure, like other Mudskippers. Most of the PCG showed similar codon usage bias. The gene length was found to be different specially for the CR, 12S rRNA gene and ND5 gene in some taxon. All the Boleophthalmus species showed a gene duplication in the CR, except for B. dussumieri, and they presented a long intergenic spacer specially on the tRNA-Pro/ OH Tandem duplication/random loss (TDRL) and dimer-mitogenome and nonrandom loss (DMNL) are suitable to explain the mitogenome rearrangement observed in this study. The phylogenetic analysis well supported the monophyly of all mudskipper species and the analysis positioned the Periophthalmus clade as the most basal of the terrestrial fishes. This finding provides basis and brings insights for gene variation, gene rearrangements and replications showing evidence for variety of mitochondrial structure diversity within mudskippers.

In this study, we present chromosome-level genome assemblies for two softshell turtles, the spiny softshell (Apalone spinifera) and the wattle‑necked softshell (Palea steindachneri), and use population level resequencing to characterize their ZW sex chromosomes. Our results indicate that W‑chromosome degeneration in these species is associated primarily with a dramatic accumulation of transposable elements (TEs)-not with stepwise strata formation as seen in many birds and mammals-and that TE proliferation likely contributed to recombination suppression between Z and W. Specifically, the pseudoautosomal regions span 0-3.17 Mb in A. spinifera and 36.74-39.62 Mb in P. steindachneri, reflecting conserved synteny; protein-coding W-linked genes show a mean dN/dS ≈ 0.52, consistent with ongoing purifying selection; and TEs occupy 73.7%-83.3% of the W sequence, with LTRs (≈22.7%-23.3%) and LINEs (≈27.9%-34.7%) markedly enriched relative to the Z chromosome and autosomes. Molecular dating of LTR insertions places most activity within the past ∼40 million years, after species divergence and temporally consistent with the inferred onset of recombination suppression. Together, these findings support a model in which large-scale TE accumulation drove rapid W‑chromosome differentiation in softshell turtles, offering a complementary pathway to strata-based sex‑chromosome evolution and underscoring the potent role of mobile elements in shaping vertebrate sex chromosomes.

Ultrastructural immunolocalization of alpha-keratins and associated beta-proteins (beta-keratins) suggests a new interpretation on the process of hard and soft cornification in turtle epidermis

Supplementary material from "Thermosensitive sex chromosome dosage compensation in ZZ/ZW softshell turtles, Apalone spinifera"